Hi,
Follow this tutorial to know how to resolve this issue
http://ambermd.org/tutorials/basic/tutorial4b/.
>From where did you get the parameters for small molecule?
IF you haven't done this, then follow the link it will teach you how to do it.
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: Manjula Saravanan [mailto:manjusimba.gmail.com]
Sent: Tuesday, February 21, 2017 12:18 PM
To: amber.ambermd.org
Subject: [AMBER] tleap error
Dear Sir,
I am trying to create topology and co-ordinates files for my ligand. After loading the ligand in tleap usong *loadmol2 *command, I have used *check* command. This gives me the following error,
AMBER General Force Field for organic molecules (Version 1.7, Nov 2013)
> LIG=loadmol2 lig4.mol2
Loading Mol2 file: ./lig4.mol2
Reading MOLECULE named complex.pdb
> check LIG
Checking 'LIG'....
Warning: Close contact of 1.471324 angstroms between .R<LIG 1>.A<H 37> and .R<LIG 1>.A<H 55> Checking parameters for unit 'LIG'.
Checking for bond parameters.
Checking for angle parameters.
*Could not find angle parameter: ss - cd - c* There are missing parameters.
check: Warnings: 1
Unit is OK.
Kindly help me in this regard.
*With Best Regards*
*S. Manjula*
*Research Scholar*
*Laboratory of Biocrystallography and Computational Molecular Biology* *Department of Physics* *Periyar University*
*Salem-11*
*Tamilnadu*
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Received on Tue Feb 21 2017 - 02:30:02 PST
